When you are plotting single point, you need to use marker.
%Node 1
x1=-419;y1=-341;z1=30;
z2=15; z3=0;
hold on
plot3(x1,y1,z1,'s')
hold on
plot3(x1,y1,z2,'s')
hold on
plot3(x1,y1,z3,'s')
hold off
You can plot whay you want using scatter3. Read about it.
%Node 1
x1=-419;y1=-341;z1=30;
z2=15; z3=0;
x = repelem(x1,3,1) ;
y = repelem(y1,3,1) ;
z = [z1;z1;z3] ;
scatter3(z,y,z,1000,z,'.');
